This is a SNP pileup vcf output based on 4 (Sanger) sequences. These 4 sequences have some overlapping sequences, but not all. I have 2 questions about how to interpretate the information.
Q1. For sample B.bam and C.bam, since PL=60,3,0, why GT is determined as 0/1, not 1/1?
Q2. sample D.bam, PL=0,0,0, how GT is determined as 0/1? Does it mean this sequence does not cover this fragment?
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A.bam B.bam C.bam D.bam
chr_6 40288662 . TTA TTATA 69.5 . INDEL;DP=5;AF1=0.4001;AC1=8;DP4=3,0,2,0;MQ=60;FQ=71.7;PV4=1,1,1,1 GT:PL:GQ 0/0:0,3,52:5 0/1:60,3,0:5 0/1:60,3,0:5 0/1:0,0,0:3
Q1. For sample B.bam and C.bam, since PL=60,3,0, why GT is determined as 0/1, not 1/1?
Q2. sample D.bam, PL=0,0,0, how GT is determined as 0/1? Does it mean this sequence does not cover this fragment?
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A.bam B.bam C.bam D.bam
chr_6 40288662 . TTA TTATA 69.5 . INDEL;DP=5;AF1=0.4001;AC1=8;DP4=3,0,2,0;MQ=60;FQ=71.7;PV4=1,1,1,1 GT:PL:GQ 0/0:0,3,52:5 0/1:60,3,0:5 0/1:60,3,0:5 0/1:0,0,0:3